Although mass spectrometric disulfide mapping is potentially fast, the experimental results are usually analyzed manually - a time-consuming task even for small proteins and prohibitively so for larger proteins. Computer programs have been written to simplify the analysis, but these only provide partial solutions to the disuffide mapping problem. We have developed a general software tool for the complete analysis of mass spectrometric disulfide mapping experiments. The tool is publicly available on the World Wide Web as a part of the PROWL environment (URL http://cbait-sgi-rockefeller.edu/). The algorithm allows for rapid disulfide linkage mapping of proteins that have undergone complete or partial digestion using enzymes with either high or low specificity. In addition, the algorithm allows for the incorporation of data from mass spectrometric fragmentation experiments as well as information from experiments involving chemical modifications such as reduction and alkylation. A paper describing the tool is in press in CABIOS.